I have the same issue — did a copy to my local server for test and development.
Only the home page will display all others “NOT FOUND ” error
One thing I did notice is that the site dB has ALL the wp_xxx names changed
i.e. no wp_options instead there is a wp_55prj3_options
I am running Nirvana (w/Cryout Plugin for Config) theme and using UM, JetPack, if Menu and Dynamic Widgets plugins
Apparently there is something UM that holds original site path for pages
Let me know what you find